[gmx-users] Reg: Adding multiple molecules

[vinothkumar mohanakrishnan]

Hi justin

if genbox is not able to find sufficient space then why should one calculate
number density for the given box dimension?.similarly the  the number of
molecules are not getting updated in the molecules section of the topology
file when inserting multiple molecules using the genbox command. everytime i
need to update it manually.is there a way to update it automatically?

Regards
Vinoth

On Mon, Sep 27, 2010 at 4:31 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> vinothkumar mohanakrishnan wrote:
>
>> Hi all
>>
>> I have a diffculty in adding multiple molecules of hexane to my box. my
>> box size is 4.72*2.36*2.36 (nm) according to my number density calculations
>> the box should fit 124 molecules of hexane whereas it adds only 76 molecules
>> to the box below is my command. i had evev tried with -try command but
>> without sucess.
>>
>> genbox -cp hexane-box.gro -ci hexane.gro -p hexane.top -o hexane-multi.gro
>> -nmol 124 -seed 1268
>>
>>
> If you're not getting all the molecules you want, then genbox is unable to
> find sufficient space for them.  Try a larger box, then equilibrate.
>
> -Justin
>
>  Regards
>> Vinoth
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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